Yes, master plugin should go first but the general position of the plugin/s isn’t really important as long as you make sure you have all the needed patches installed. You can totally put it high in the load order.
I found that blackthorne is flagged as generic in the vanilla game-unrelated to this mod- Is there a way to get her to behave like a normal essential npc and be unique?
I'm not sure if I fully understood the question, but the mod marks her as unique and she has a protected status (i.e. can be only killed by the player) in both vanilla and the mod. If what you mean is how you could keep her unique without having the mod in your load order, if you're versed in using tes5edit you could basically just pull it up, copy over the changes made by the mod into a separate plugin, and change the 'protected' flag to 'essential'. Although idk what would be the use for that as in vanilla she disappears from the game after the first time you meet her. Alternatively, if you just want to make her essential with the mod loaded, just use 'set essential [her refid] 1' in the command console.
Absolutely, fully safe to merge. However, if you're using the tes5edit script to do it I would kind of suggest checking for errors afterwards in case something goes awry in the process. Can happen with any kind of merge, really.
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Everyone should download :D
Is there a way to get her to behave like a normal essential npc and be unique?
I wish I would've known this mod before one of my characters got married and had kids, I use beeing female